Sequencing Florida panther genome<\/strong><\/h2>\n\n\n\nThe NC State University Genomic Sciences Laboratory (GSL) partnered with High School students in Milton, Florida to sequence the genome of the rare and endangered Florida panther (Puma concolor coryi<\/em>), an isolated population of the North American cougar or mountain lion (Puma concolor<\/em>). Currently, only 120-230 Florida panthers are thought to exist, and are located largely south of Lake Okeechobee in the natural habitat of the Florida Everglades and Big Cypress Region. These animals ranged historically throughout Florida and other parts of the southeastern United States. The Florida panther is currently under the protection of the Endangered Species Act1<\/sup>.<\/p>\n\n\n\n <\/figure>\n\n\n\nThe Florida panther is the mascot of Milton High School, located in the small town of Milton, Florida in Santa Rosa County of the Florida Panhandle. Sam Rezell, a Milton High School science teacher, partnered with a former Milton High School alumnus, Mike Kreitzinger, who is currently a regional sales director for Illumina, Inc. Illumina is a San Diego-based genomics company whose mission is the unlock the power of the genome to improve human health. Rezell and Kreitzinger partnered with Dr. Dave Onorato of the Florida Fish & Wildlife Conservation Commission (FWC) to host a three-day sequencing workshop at Milton High School in which students learned about the significance and applications of DNA sequencing, as well as gained hands-on experience with pipetting and DNA sequencing procedures. As a final component of the workshop, Illumina lent a MiSeq System so students could sequence the actual genome of a real Florida panther, identified as FP20 by FWC panther biologists2<\/sup>.<\/p>\n\n\n\nPanther FP20 was initially captured and radio collared by FWC in March of 1987. He was subsequently injured in a vehicle collision in June of 1987. FP20 was treated and rehabilitated at Miami Metro Zoo (now Zoo Miami) until August of 1987, when he was released back into the wild (Fig. 1). FP20 lived for another year, and died in the wild in August of 1988, from issues associated with a heart condition (atrial septal defect) found to be prevalent in Florida panthers during that era due to inbreeding depression3<\/sup>. A sample of DNA was taken during his convalescence at the Miami Metro Zoo, and this was used for the Florida panther genome sequencing efforts. In addition to<\/p>\n\n\n\nproviding invaluable research experience for Milton High School students, enabling them to perform cutting-edge research on their school mascot, the sequenced Florida panther genome has enormous potential to enhance conservation efforts for this species. In a collaborative effort, the GSL facility at NC State University has agreed to provide additional sequencing data for this project, in order to generate a high-quality reference genome that can be used to better understand the population structure of Florida panthers in the wild, develop better forensic testing methods to protect the status of this endangered animal, and to foster a greater understanding of animal diseases in the wild.<\/p>\n\n\n\n <\/figure>\n\n\n<\/div>\n\n\n\n
Genomic Resources For Sweet Potato Improvement<\/h2>\n\n\n\nYencho Lab<\/h4>\n\n\n\n Sweetpotato is the seventh most important food crop due to its high adaptability to tropical, subtropical and temperate climates. Its low glycemic index, high fiber content and nutraceutical content is making it popular in the chip and French fry industry. It is a critical food and health security crop in many developing countries, especially in sub-Saharan Africa. Its wide adoptability is still limited by cultural preference for specific culinary and agronomic traits and challenges due to its polyploid nature and resulting complex trait inheritance.<\/p>\n\n\n\n <\/figure>\n\n\n\nWith funding support from the Bill and Melinda Gates Foundation Genomic Tools for Sweetpotato (GT4SP) Improvement Project and Illumina, Inc., Greater Good Initiative we are developing genomic resources for this autoallopolyploid. These include: (i) reference genome assemblies of two of sweetpotato\u2019s wild diploid progenitors; and (ii) an optimized sequencing-based genotyping protocol and analysis pipeline that provides accurate dosage calls, minimal missing data and high-fidelity SNPs. Ongoing efforts to generate additional genomic resources include: (i) reference genome assembly of tropical- and temperate-adapted hexaploid sweetpotato genomes; and (ii) developing a SNP panel (for a SNP array or targeted sequencing-based genotyping) with minimal ascertainment bias. These will be derived from our ongoing effort to provide high-density DNA markers for the germplasm collection representing the global diversity of the crop.<\/p>\n\n\n
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<\/figure><\/div>\n\n\nBeyond the generation over 20 Tb of sequencing data, we hope to provide insights into fundamental biological questions and show how these resources can be routinely deployed in breeding programs. Currently, some of our studies include understanding the genetic basis for rapid climatic adaptation of crops and the genomic features that are perturbed during this process. Using dosage information of polyploid genotypes, we are constructing linkage maps and performing QTL and genome-wide association analysis for several important traits. Results from these studies will encourage use of marker-assisted and genomic selection in sweetpotato breeding programs worldwide.<\/p>\n\n\n